CopomuS - ranking compensatory mutations to guide RNA-RNA interaction verification experiments
Abstract: In silico RNA-RNA interaction prediction is widely applied to identify putative interaction partners and to assess interaction details in base pair resolution. To verify specific interactions, in vitro evidence can be obtained via compensatory mutation experiments. Unfortunately, the selection of compensatory mutations is non-trivial and typically based on subjective ad hoc decisions. To support the decision process, we introduce our COmPensatOry MUtation Selector CopomuS. CopomuS evaluates the effects of mutations on RNA-RNA interaction formation using a set of objective criteria, and outputs a reliable ranking of compensatory mutation candidates. For RNA-RNA interaction assessment, the state-of-the-art IntaRNA prediction tool is applied. We investigate characteristics of successfully verified RNA-RNA interactions from the literature, which guided the design of CopomuS. Finally, we evaluate its performance based on experimentally validated compensatory mutations of prokaryotic sRNAs and their target mRNAs. CopomuS predictions highly agree with known results, making it a valuable tool to support the design of verification experiments for RNA-RNA interactions. It is part of the IntaRNA package and available as stand-alone webserver for ad hoc application
- Location
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Deutsche Nationalbibliothek Frankfurt am Main
- Extent
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Online-Ressource
- Language
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Englisch
- Notes
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International journal of molecular sciences. - 21, 11 (2020) , 3852, ISSN: 1422-0067
- Event
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Veröffentlichung
- (where)
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Freiburg
- (who)
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Universität
- (when)
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2020
- DOI
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10.3390/ijms21113852
- URN
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urn:nbn:de:bsz:25-freidok-1663261
- Rights
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Der Zugriff auf das Objekt ist unbeschränkt möglich.
- Last update
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25.03.2025, 1:51 PM CET
Data provider
Deutsche Nationalbibliothek. If you have any questions about the object, please contact the data provider.
Associated
- Raden, Martin
- Gutmann, Fabio
- Uhl, Michael
- Backofen, Rolf
- Universität
Time of origin
- 2020
Other Objects (12)
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Ant colony optimization based inverse folding of mono- and bistable RNA macromolecules
Interactive implementations of thermodynamics-based RNA structure and RNA–RNA interaction prediction approaches for example-driven teaching
Integration of accessibility data from structure probing into RNA–RNA interaction prediction
MutaRNA: analysis and visualization of mutation-induced changes in RNA structure
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Computational analysis and prediction of RNA-RNA interactions : = Computergestützte Analyse und Vorhersage von RNA-RNA-Interaktionen
INFO-RNA—a server for fast inverse RNA folding satisfying sequence constraints
Using local RNA secondary structures for computational comparison and clustering of RNA molecules
Expressivity and decidability of first-order languages over feature trees
Expressivity and decidability of first-order languages over feature trees
IntaRNA 2.0: enhanced and customizable prediction of RNA–RNA interactions
Ant colony optimization based inverse folding of mono- and bistable RNA macromolecules
Interactive implementations of thermodynamics-based RNA structure and RNA–RNA interaction prediction approaches for example-driven teaching
Integration of accessibility data from structure probing into RNA–RNA interaction prediction
MutaRNA: analysis and visualization of mutation-induced changes in RNA structure
CRISPRtracrRNA: robust approach for CRISPR tracrRNA detection